search

jfnavarro / st_analysis

A toolset for analysis and visualisation of Spatial Transcriptomics datasets.
Other
18 stars 7 forks source link

Preprocess Normalization #43

Open minhtran1309 opened 4 years ago

minhtran1309 commented 4 years ago

Hi, I found two repositories for st_analysis and quite confused which one is the latest and updated one. Anyway, my issue is that I want to make use of several RNA-seq count matrix, but there is no function that could perform TMM normalization or Sum Factors normalization from this repo. Whereas, the other repo which has been updated for 2 years, does have those function I need. However, most library modules are outdated and no longer be supported like py2ri().
For example:

n_cells = len(counts.columns)
pandas2ri.activate()
r_counts = pandas2ri.py2ri(counts)
scran = RimportLibrary("scran")
multicore = RimportLibrary("BiocParallel")
multicore.register(multicore.MulticoreParam(multiprocessing.cpu_count()-1))